An intensive effort was directed toward examining the relationships between changes in viral burden, changes in viral genotype and phenotype, and changes in immunologic function in patients with human immunodeficiency virus (HIV) infection receiving a variety of anti- retroviral agents with different mechanisms of action given alone or in combination. Interestingly, the majority of patients entering studies of new anti-retroviral agents did so with viral isolates containing mutations indicative of prior zidovudine exposure. The response to combination anti-retroviral therapy using 3 reverse transcriptase inhibitors simultaneously was clearly worse in those patients with a pre- existing mutation at the 215 codon. The patterns of viral resistance that emerged in vivo were quite distinct from those generated in vitro. Studies of the immunotoxin CD4-Pseudomonas exotoxin (CD4-PE) were conducted for the first time in humans. RNA-based methods were evaluated for the monitoring of viral burden. An infectious clone of HIV underwent an 8-base pair insertion in the region of the long terminal repeat. This mutant virus was replication competent and served as an excellent internal control for the measurement of particle-associated RNA in plasma. The branched-DNA (bDNA) technique was found capable of quantitatively measuring changes in viral burden in large numbers of samples to a significantly greater degree than existing techniques. The rate of CD4 count decline in a cohort of patients managed with combination anti-retroviral therapy was determined to be related to baseline levels of HIV RNA.